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Tophat Reporting Output Step Is Very Slow

Hi,

For on of my samples, tophat 2 is stuck into the reporting output step. In the tmp/ directory, it seems that the accepted_hits.bam is currently been constructed (but very very slowly). It's strange because on my other samples, it works well. And this sample is not different compared to the other (in size).

FYI, I use tophat 2.0.0.3 with bowtie 2 beta 6

Anyone has an idea to resolve this problem ..

Thanks,

N.

tophat
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updated by Biostar Biostar • written by Nicolas Rosewick Nicolas Rosewick

1 answer

Still running and accepted_hits.bam still in construction , so I guess tophat execution is fine but I've no idea why it takes so long to report output (now it's been 4 days...)

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written by Nicolas Rosewick Nicolas Rosewick

how many threads are you using, and what reference genome are you mapping against? Is this genome different than ones you have used previously?

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written by Dan D Dan D

I contact the author of tophat 2 and he resolved the problem in the last release :)

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written by Nicolas Rosewick Nicolas Rosewick

Please tell us about it so that this thread can have some value the next time this problem arises.

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written by karl.stamm karl.stamm

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